Hi Dear AMBER USERS
I have perform the Implicit simulation of protein and
drug molecule, Further i would like to calculate the binding energy using
MMPBSA and GB method but the most of tutorial show the explicit simulation
data for MMPBSA/GB calculation.
like this
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y
*.mdcrd.
my question is that, it is possible to perform the PB and GB calculation
without the solvated.prmtop file.
Please suggest me how to do this.
Thanks
Bajarang
--
*Dr. Bajarang V. Kumbhar* M.Sc.
Ph.D
Post-Doctoral Fellow
Lab-204, Biophysics and Computational Biology,
Department of Biosciences and Bioengineering,
Indian Institute of Technology Bombay, Powai Mumbai-400076
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Received on Sat Nov 08 2014 - 22:30:02 PST
